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Magnesium in PDB 3juk: The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose

Enzymatic activity of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose

All present enzymatic activity of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose:
2.7.7.9;

Protein crystallography data

The structure of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose, PDB code: 3juk was solved by H.Kim, K.K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.444, 74.393, 167.123, 90.00, 97.91, 90.00
R / Rfree (%) 23 / 27.6

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose (pdb code 3juk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose, PDB code: 3juk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3juk

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Magnesium binding site 1 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.3
occ:1.00
 OD1 A:ASP130 2.2 21.0 1.0
O1B A:UPG282 2.3 19.2 1.0
O A:HOH346 2.3 21.2 1.0
O2A A:UPG282 2.3 21.1 1.0
O A:HOH359 2.4 17.5 1.0
O A:HOH338 2.5 9.2 1.0
CG A:ASP130 3.3 20.7 1.0
PA A:UPG282 3.5 22.3 1.0
PB A:UPG282 3.5 19.9 1.0
NZ A:LYS25 3.7 22.3 1.0
O3A A:UPG282 3.8 22.0 1.0
OD2 A:ASP130 3.9 21.5 1.0
O A:HOH360 3.9 23.2 1.0
O A:HOH348 4.0 25.4 1.0
CA A:GLY256 4.1 20.3 1.0
O6' A:UPG282 4.2 19.5 1.0
O2B A:UPG282 4.2 18.0 1.0
OD2 A:ASP254 4.3 22.0 1.0
O1A A:UPG282 4.3 21.4 1.0
CB A:ASP130 4.4 18.9 1.0
O5C A:UPG282 4.5 22.0 1.0
O3B A:UPG282 4.6 18.0 1.0
C5C A:UPG282 4.6 21.4 1.0
O5' A:UPG282 4.6 15.9 1.0
O A:HOH389 4.7 10.4 1.0
CE A:LYS25 4.7 24.3 1.0
C A:GLY256 4.8 22.7 1.0
O A:GLY256 4.9 22.6 1.0
C1' A:UPG282 5.0 16.1 1.0
N A:GLY256 5.0 21.5 1.0

Magnesium binding site 2 out of 12 in 3juk

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Magnesium binding site 2 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:20.4
occ:1.00
 CG1 A:VAL258 3.3 27.4 1.0
N A:VAL258 4.0 22.9 1.0
CB A:SER257 4.2 19.7 1.0
N A:GLU259 4.2 26.0 1.0
CB A:VAL258 4.6 24.9 1.0
CB A:GLU259 4.6 26.9 1.0
CA A:SER257 4.7 22.0 1.0
C A:SER257 4.7 22.3 1.0
CA A:VAL258 4.7 24.8 1.0
OG A:SER257 4.9 21.5 1.0
CD A:ARG15 5.0 35.9 1.0
C A:VAL258 5.0 24.9 1.0

Magnesium binding site 3 out of 12 in 3juk

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Magnesium binding site 3 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:31.6
occ:1.00
 O A:HOH389 3.3 10.4 1.0
N A:THR14 3.5 25.7 1.0
O A:HOH360 3.6 23.2 1.0
N A:ARG15 3.7 27.4 1.0
O A:HOH355 3.9 28.6 1.0
CZ A:ARG15 3.9 43.7 1.0
NH1 A:ARG15 3.9 44.6 1.0
CB A:THR14 4.0 26.0 1.0
C A:GLY13 4.1 25.9 1.0
CA A:THR14 4.1 25.6 1.0
CA A:GLY13 4.2 26.2 1.0
NH2 A:ARG15 4.2 46.9 1.0
NE A:ARG15 4.3 41.5 1.0
CG A:ARG15 4.3 34.4 1.0
C A:THR14 4.4 26.2 1.0
CB A:ARG15 4.4 32.0 1.0
N A:GLY13 4.5 26.6 1.0
OG1 A:THR14 4.6 26.5 1.0
CA A:ARG15 4.7 28.7 1.0
NZ A:LYS25 4.9 22.3 1.0
O A:GLY13 4.9 25.7 1.0
CD A:ARG15 4.9 35.9 1.0

Magnesium binding site 4 out of 12 in 3juk

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Magnesium binding site 4 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:36.5
occ:1.00
 OD1 B:ASP130 2.2 14.2 1.0
O B:HOH354 2.3 20.2 1.0
O B:HOH360 2.3 19.5 1.0
O B:HOH558 2.3 21.5 1.0
O1B B:UPG282 2.3 17.7 1.0
O2A B:UPG282 2.4 19.9 1.0
CG B:ASP130 3.0 15.1 1.0
OD2 B:ASP130 3.1 12.3 1.0
PA B:UPG282 3.5 19.5 1.0
PB B:UPG282 3.5 16.2 1.0
O6' B:UPG282 3.6 16.0 1.0
O3A B:UPG282 3.6 18.4 1.0
NZ B:LYS25 3.9 27.9 1.0
O5' B:UPG282 4.0 15.5 1.0
C5C B:UPG282 4.1 18.5 1.0
O5C B:UPG282 4.2 19.2 1.0
O3B B:UPG282 4.3 17.1 1.0
CB B:ASP130 4.4 14.5 1.0
O B:HOH309 4.4 14.3 1.0
OD2 B:ASP254 4.4 20.1 1.0
O2B B:UPG282 4.5 19.7 1.0
C1' B:UPG282 4.5 14.8 1.0
O1A B:UPG282 4.5 17.2 1.0
CA B:GLY256 4.6 17.8 1.0
O B:HOH346 4.6 29.4 1.0
C5' B:UPG282 4.6 15.3 1.0
C6' B:UPG282 4.6 15.9 1.0
O B:HOH407 4.8 17.6 1.0
CE B:LYS25 4.9 27.0 1.0

Magnesium binding site 5 out of 12 in 3juk

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Magnesium binding site 5 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:33.2
occ:1.00
 O A:HOH648 2.9 48.3 1.0
NH2 A:ARG272 3.5 45.8 1.0
CG2 B:VAL258 3.6 26.9 1.0
N B:VAL258 3.7 20.9 1.0
N B:GLU259 3.8 26.0 1.0
CB B:SER257 4.0 16.0 1.0
CB B:GLU259 4.3 28.9 1.0
CB B:VAL258 4.3 25.1 1.0
C B:SER257 4.4 20.6 1.0
CA B:VAL258 4.4 24.5 1.0
CA B:SER257 4.4 19.1 1.0
CG1 B:VAL258 4.4 23.8 1.0
CZ A:ARG272 4.6 47.5 1.0
C B:VAL258 4.6 25.3 1.0
OG B:SER257 4.6 16.9 1.0
CA B:GLU259 4.7 26.3 1.0
NH1 A:ARG272 4.9 46.9 1.0

Magnesium binding site 6 out of 12 in 3juk

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Magnesium binding site 6 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:31.5
occ:1.00
 N B:ARG15 3.4 27.1 1.0
N B:THR14 3.6 26.0 1.0
O B:HOH346 3.6 29.4 1.0
O B:HOH361 3.7 18.7 1.0
CD B:ARG15 3.7 33.6 1.0
CB B:ARG15 3.8 29.4 1.0
NH2 B:ARG15 4.0 38.3 1.0
CB B:THR14 4.0 26.1 1.0
C B:GLY13 4.0 26.4 1.0
CA B:THR14 4.2 26.0 1.0
CA B:ARG15 4.2 27.9 1.0
CA B:GLY13 4.2 25.9 1.0
O B:HOH331 4.2 21.5 1.0
C B:THR14 4.3 26.9 1.0
NE B:ARG15 4.4 36.3 1.0
CG B:ARG15 4.5 30.5 1.0
N B:GLY13 4.5 27.4 1.0
CZ B:ARG15 4.5 39.2 1.0
OG1 B:THR14 4.7 25.1 1.0
O B:GLY13 4.8 24.2 1.0

Magnesium binding site 7 out of 12 in 3juk

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Magnesium binding site 7 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg307

b:19.8
occ:1.00
 OD1 C:ASP130 2.1 16.6 1.0
O C:HOH430 2.2 11.8 1.0
O1B C:UPG283 2.3 16.0 1.0
O C:HOH326 2.3 17.8 1.0
O C:HOH356 2.4 13.2 1.0
O2A C:UPG283 2.4 15.8 1.0
CG C:ASP130 3.1 17.1 1.0
PB C:UPG283 3.3 18.1 1.0
PA C:UPG283 3.3 17.9 1.0
O3A C:UPG283 3.4 18.8 1.0
OD2 C:ASP130 3.4 20.1 1.0
O C:HOH483 3.5 31.0 1.0
NZ C:LYS25 3.5 28.8 1.0
O C:HOH385 4.1 31.3 1.0
O6' C:UPG283 4.2 13.1 1.0
O2B C:UPG283 4.2 18.2 1.0
O5C C:UPG283 4.2 16.8 1.0
C5C C:UPG283 4.3 16.0 1.0
CA C:GLY256 4.3 19.8 1.0
O1A C:UPG283 4.3 17.0 1.0
O C:HOH285 4.4 12.5 1.0
O3B C:UPG283 4.4 16.7 1.0
CB C:ASP130 4.4 15.4 1.0
O5' C:UPG283 4.5 15.2 1.0
OD2 C:ASP254 4.5 26.0 1.0
CE C:LYS25 4.5 28.0 1.0
C1' C:UPG283 4.8 15.8 1.0
O C:HOH296 5.0 8.0 1.0

Magnesium binding site 8 out of 12 in 3juk

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Magnesium binding site 8 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg308

b:26.4
occ:1.00
 N C:ARG15 3.8 22.0 1.0
N C:THR14 3.9 23.2 1.0
O C:HOH296 3.9 8.0 1.0
CB C:ARG15 4.0 26.2 1.0
CB C:THR14 4.1 20.8 1.0
O C:HOH483 4.3 31.0 1.0
CA C:THR14 4.4 21.9 1.0
NE C:ARG15 4.4 31.1 1.0
NH2 C:ARG15 4.4 34.2 1.0
C C:GLY13 4.4 23.6 1.0
C C:THR14 4.5 22.6 1.0
CA C:GLY13 4.5 23.0 1.0
CA C:ARG15 4.6 23.2 1.0
N C:GLY13 4.7 24.2 1.0
OG1 C:THR14 4.7 21.5 1.0
CZ C:ARG15 4.8 34.3 1.0

Magnesium binding site 9 out of 12 in 3juk

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Magnesium binding site 9 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg309

b:25.0
occ:1.00
 CG1 C:VAL258 2.9 31.1 1.0
OG C:SER257 3.3 29.7 1.0
N C:VAL258 3.7 25.4 1.0
NH1 C:ARG15 3.7 33.8 1.0
N C:GLU259 3.9 28.6 1.0
CB C:VAL258 4.1 28.1 1.0
CA C:VAL258 4.3 27.5 1.0
CB C:SER257 4.4 24.4 1.0
CB C:GLU259 4.5 30.8 1.0
CD C:ARG15 4.5 29.7 1.0
C C:SER257 4.6 25.1 1.0
CA C:SER257 4.6 23.9 1.0
C C:VAL258 4.7 27.1 1.0
CA C:GLU259 4.8 28.5 1.0
CZ C:ARG15 4.9 34.3 1.0

Magnesium binding site 10 out of 12 in 3juk

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Magnesium binding site 10 out of 12 in the The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Crystal Structure of Udp-Glucose Pyrophosphorylase Complexed with Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg310

b:35.5
occ:1.00
 OD2 D:ASP130 2.1 10.8 1.0
O D:HOH387 2.2 14.6 1.0
O1B D:UPG284 2.3 16.5 1.0
O D:HOH559 2.4 30.4 1.0
O D:HOH367 2.4 18.7 1.0
O2A D:UPG284 2.4 22.0 1.0
CG D:ASP130 3.1 15.2 1.0
PB D:UPG284 3.5 18.4 1.0
PA D:UPG284 3.5 22.8 1.0
O6' D:UPG284 3.5 15.3 1.0
OD1 D:ASP130 3.6 17.6 1.0
O3A D:UPG284 3.7 19.9 1.0
O D:HOH611 3.9 22.6 1.0
NZ D:LYS25 3.9 26.4 1.0
O5' D:UPG284 4.1 17.6 1.0
O D:HOH443 4.2 22.1 1.0
C5C D:UPG284 4.3 20.1 1.0
OD2 D:ASP254 4.3 23.1 1.0
O5C D:UPG284 4.3 21.4 1.0
CB D:ASP130 4.4 13.8 1.0
O3B D:UPG284 4.4 17.2 1.0
CA D:GLY256 4.4 15.5 1.0
O2B D:UPG284 4.4 19.6 1.0
O1A D:UPG284 4.5 22.5 1.0
C6' D:UPG284 4.5 17.4 1.0
C5' D:UPG284 4.5 17.7 1.0
C1' D:UPG284 4.6 16.7 1.0
O D:HOH337 4.7 29.7 1.0
CE D:LYS25 5.0 24.0 1.0

Reference:

H.Kim, J.Choi, T.Kim, N.K.Lokanath, S.C.Ha, S.W.Suh, H.-Y.Hwang, K.K.Kim. Structural Basis For the Reaction Mechanism of Udp-Glucose Pyrophosphorylase Mol.Cells V. 29 397 2010.
ISSN: ISSN 1016-8478
PubMed: 20238176
DOI: 10.1007/S10059-010-0047-6
Page generated: Wed Aug 14 17:14:08 2024

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